Literature DB >> 28231515

Computational tools for enzyme improvement: why everyone can - and should - use them.

Maximilian Ccjc Ebert1, Joelle N Pelletier2.   

Abstract

This review presents computational methods that experimentalists can readily use to create smart libraries for enzyme engineering and to obtain insights into protein-substrate complexes. Computational tools have the reputation of being hard to use and inaccurate compared to experimental methods in enzyme engineering, yet they are essential to probe datasets of ever-increasing size and complexity. In recent years, bioinformatics groups have made a huge leap forward in providing user-friendly interfaces and accurate algorithms for experimentalists. These methods guide efficient experimental planning and allow the enzyme engineer to rationalize time and resources. Computational tools nevertheless face challenges in the realm of transient modern technology.
Copyright © 2017 Elsevier Ltd. All rights reserved.

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Year:  2017        PMID: 28231515     DOI: 10.1016/j.cbpa.2017.01.021

Source DB:  PubMed          Journal:  Curr Opin Chem Biol        ISSN: 1367-5931            Impact factor:   8.822


  12 in total

1.  Filling the Void: Introducing Aromatic Interactions into Solvent Tunnels To Enhance Lipase Stability in Methanol.

Authors:  Shalev Gihaz; Margarita Kanteev; Yael Pazy; Ayelet Fishman
Journal:  Appl Environ Microbiol       Date:  2018-11-15       Impact factor: 4.792

Review 2.  Design of artificial metalloproteins/metalloenzymes by tuning noncovalent interactions.

Authors:  Shun Hirota; Ying-Wu Lin
Journal:  J Biol Inorg Chem       Date:  2017-12-07       Impact factor: 3.358

Review 3.  Engineering Thermostable Microbial Xylanases Toward its Industrial Applications.

Authors:  Vishal Kumar; Arun Kumar Dangi; Pratyoosh Shukla
Journal:  Mol Biotechnol       Date:  2018-03       Impact factor: 2.695

4.  In Silico Prediction Methods for Site-Saturation Mutagenesis.

Authors:  Ge Qu; Zhoutong Sun
Journal:  Methods Mol Biol       Date:  2022

5.  NMR-guided directed evolution.

Authors:  Eleonora G Margheritis; Katsuya Takahashi; Alona Kulesha; Sagar Bhattacharya; Areetha D'Souza; Inhye Kim; Jennifer H Yoon; Jeremy R H Tame; Alexander N Volkov; Olga V Makhlynets; Ivan V Korendovych
Journal:  Nature       Date:  2022-10-05       Impact factor: 69.504

Review 6.  A global analysis of function and conservation of catalytic residues in enzymes.

Authors:  António J M Ribeiro; Jonathan D Tyzack; Neera Borkakoti; Gemma L Holliday; Janet M Thornton
Journal:  J Biol Chem       Date:  2019-12-03       Impact factor: 5.157

7.  Bioinformatic analysis of the fold type I PLP-dependent enzymes reveals determinants of reaction specificity in l-threonine aldolase from Aeromonas jandaei.

Authors:  Kateryna Fesko; Dmitry Suplatov; Vytas Švedas
Journal:  FEBS Open Bio       Date:  2018-05-21       Impact factor: 2.693

8.  P450-BM3-Catalyzed Sulfoxidation versus Hydroxylation: A Common or Two Different Catalytically Active Species?

Authors:  Jian-Bo Wang; Qun Huang; Wei Peng; Peng Wu; Da Yu; Bo Chen; Binju Wang; Manfred T Reetz
Journal:  J Am Chem Soc       Date:  2020-01-21       Impact factor: 15.419

Review 9.  Computational Tools for Discovering and Engineering Natural Product Biosynthetic Pathways.

Authors:  Hengqian Ren; Chengyou Shi; Huimin Zhao
Journal:  iScience       Date:  2019-12-27

10.  Highly thermostable carboxylic acid reductases generated by ancestral sequence reconstruction.

Authors:  Adam Thomas; Rhys Cutlan; William Finnigan; Mark van der Giezen; Nicholas Harmer
Journal:  Commun Biol       Date:  2019-11-22
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